Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

Re: [Freesurfer] Label2label on fsaverage
by Bruce Fischl 12 Aug '11

12 Aug '11

Hi Rouhi it's hard to tell from looking at the sphere.reg by itself. In general though if the parcellations are correct then the registration must be pretty good. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: > Dear Bruce > I checked the parcellation and look quiet OK. I attached two subjects , whcih subj_1 shows bad registration to fsaverage and subj_2 shows the > good registration. I attached a file which compare two subjects according to sphere and sphere.reg. For the subj_1 , it has more figures to see > how the parcellation is. > Thanks in advance > > Best > Rouhi > > On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Rouhi > > check the parcellations. If they are correct then the sphere.reg must be pretty accurate. > > cheers > Bruce > > On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: > > Dear Bruce > > I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create > caret surfaces. when I look at my subjects' > surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to > sphere registration to fsaverage sphere. Beacsue > the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good > data (3 subjects) but for the (9 subjects) > rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that > sphere.reg properly created? > > Thank you very much > > Rouhi > > > > On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Try using fsaverage as the trgsubject > Cheers > Bruce > > > > On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466(a)gmail.com> wrote: > > > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the > output label file on fsaverage surface > like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to > fsaverage or something esle? The question is > how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 > Content-Type: text/html; > charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > > > I've tried to export my label file from individual space to fsaverage space by using this command: > > > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > > like it is not deformed properly. > > Is it related to registration to fsaverage or something esle? > > The question is how I can register the subjects surfaces to fsaverage > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > > -- > With Best Regards > Rouhollah Abdollahi > > > > > > > > -- > With Best Regards > Rouhollah Abdollahi > > > > >

1 0

Flipping analyze images
by Catherine Wan 12 Aug '11

12 Aug '11

Dear List, I have a question regarding using .img in Freesurfer. We only have analyze images, but we can tell the orientation of the images through the patient's lesion location. Because freesurfer sometimes flips these image after recon-all, I'm now flipping the "problematic" ones using mri_convert <input> --out_orientation RAS <output> before running them again. Could someone please explain why if we use analyze images, some of them would be flipped by Freesurfer but not others? Does that only apply to lesioned/patient brains and not normal brains? Many thanks! Catherine

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nu_correct error
by Todd Krieg 11 Aug '11

11 Aug '11

To whom it may concern, I am having trouble running recon-all. I keep getting an error that nu_correct is not found. 'which nu_correct' return nothing. Here is the information: bugr output: FREESURFER_HOME: /home/mogul/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.35-22-generic x86_64 which recon-all /home/mogul/freesurfer/bin/recon-all Current working directory is ~ (/home/mogul) - aka root Command line ran: recon-all -s bert -autorecon1 Main error message received is: nu_correct: Command not found. ERROR: nu_correct recon-all.log file attached for additional information. I even uninstalled freesurfer and re-installed it with the same problem. Any help you could offer would be much appreciated. Thank you for your time. ---Todd Krieg tkrieg(a)hawk.iit.edu

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Brodmann areas stats table
by _andreia_＠sapo.pt 11 Aug '11

11 Aug '11

FreeSurfers, Is there a way to get BA cortical thickness in a table to export from FS? As there is for aseg and aparc stats. Thanks! Andreia -- Andreia Pereira, MSc student Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-354 Coimbra Portugal Phone +(351) 239480220 Fax +(351) 239480280

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Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer
by Douglas N Greve 11 Aug '11

11 Aug '11

I'm not sure what you would visualize. These are just single numbers per subject. doug Knut J Bjuland wrote: > Hi > > Is is possible to visualize this data on sub-cortical structure in wya > similar to the aging tutorial? > > Knut J > > On 08/11/2011 09:03 PM, Douglas N Greve wrote: > >> use --segno 10 --segno 49 >> These codes are from $FREESURFER_HOME/FreeSurferColorLUT.txt and >> correspond to left and right thalamus. Use -m volume to get the volume >> of thalamus (this is the default). If you're only looking at one >> measure, then no correction for multiple comparisons is necessary. You >> can test the effect of gender by loading this output into a stats >> program or using mri_glmfit with the --table option. >> doug >> >> Knut J Bjuland wrote: >> >>> Hi Bruce >>> >>> I am now responding to the list as well. I have a group with different >>> subjects where I wish to correlate thalamus volume with gender >>> difference. Though I have extract the data using asegstats2table. I wish >>> to be sure that the group difference is correct. Due to this reason I >>> wish to use multiple comparsion within Freesurfer for instant FDR. I >>> have some trouble figuring out --iv volmeasfile or how to use an label >>> to include thalamus but exclude everything else? >>> >>> Knut J >>> >>> >>> Knut J >>> >>> On 08/11/2011 08:42 PM, Bruce Fischl wrote: >>> >>> >>>> Hi Knut >>>> >>>> you should respond onlist so Doug and Nick can answer! If all you want >>>> is thalamic volume then why do you have multiple comparisons? You only >>>> have one number/subject, no? >>>> Bruce >>>> >>>> On Thu, 11 Aug 2011, Knut J Bjuland wrote: >>>> >>>> >>>> >>>>> Hi Bruce >>>>> >>>>> I wish to use a group difference analysis using gender and correlate >>>>> thalamus volume with IQ, and then apply multiple comparisons using FDR >>>>> or Monte Carlo simulation. Do you have any links to a good tutorial? I >>>>> inted to use mris_preproc and mris_glm for voulmetirc analysis, but I >>>>> have some trouble figuring out --iv volmeasfile? >>>>> >>>>> Cheers >>>>> Knut J >>>>> >>>>> >>>>> Knut J >>>>> >>>>> On 08/11/2011 08:03 PM, Bruce Fischl wrote: >>>>> >>>>> >>>>>> Hi Knut >>>>>> >>>>>> you don't need to register it since the segmentation (aseg) is >>>>>> created >>>>>> from the same data as the surface. What kind of analysis are you >>>>>> thinking of doing? >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Thu, 11 Aug 2011, Knut J Bjuland wrote: >>>>>> >>>>>> >>>>>> >>>>>>> I am working to do a volumetric analysis in Freesurfer using >>>>>>> Thalamus. I >>>>>>> do not know if this is the correct way to go. Should I first >>>>>>> register >>>>>>> thalamus to a surface using tkregister? There was also another >>>>>>> post on >>>>>>> this list, which suggested using tkregister2? I am also search to >>>>>>> find >>>>>>> a tutorial on how to create a volmask and the use it to calculate >>>>>>> statistic in Freesurfer for Thalamus. >>>>>>> >>>>>>> Knut J >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom >>>>>> it is >>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>> the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>> you >>>>>> in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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tksurfer & rtview
by Michelle Umali 11 Aug '11

11 Aug '11

Hi Doug, The z-values are consistently near or greater than 4. It just seems that the visualization of the angles is somehow incorrect... Is there be anything else that I need to check? Thanks. Michelle

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registration issues with lesioned brains and kids' brains
by Catherine Wan 11 Aug '11

11 Aug '11

Dear Freesurfer-list, I have 2 questions: one regarding lesioned brains and another regarding kids’ brains. 1) All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis? 2) We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz –s --fstal --surf orig and found that the green line didn’t cover the surfaces well in most cases (see attached) . I’ve read in previous postings that Freesurfer should be fine with kids’ brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions? Many thanks in advance for your help! Regards, Catherine

2 4

recon-all and corrected hemispheres
by Ayaz, Muhammad 11 Aug '11

11 Aug '11

Dear All, I acquired the images using Phillips scanner. I converted the images from par into analyze using MRIcro. I noticed that images were flipped when I view them in the axial plane, i.e. when I look at the images on the computer screen the Right hemisphere (where we tapped the fish oil tablet) is on the right side of the image. Should I flip the images before running through the recon-all? Thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Re: [Freesurfer] long_mris_slopes error
by Martin Reuter 11 Aug '11

11 Aug '11

Hi Hyojeong, on the wiki release notes is a fixed mris_calc binary. Best, Martin On Aug 11, 2011, at 8:00 AM, Administrator wrote: > Dear Martin, > > I've received the same error as below which discussed previously. > Would you tell me if you managed build a fixed file, please? > > Hyojeong Lee > Hallym University College of Medicine, Anyang, Korea > > > long_mris_slopes --qdec ./qdec/long.qdec.tem_VNL01_KCY.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks --qcache fsaverage > ...... > =============================================================================== > SUBJECT VN1 fwhm 0 computing SPC > > mris_calc -o /Volumes/data/freesurfer_analysis/VN_longitudinal/VN1/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-VN1_lh_thickness_OLudiD/beta1.mgh div ./tmp-VN1_lh_thickness_OLudiD/beta0.mgh > > ERROR -10 : mris_calc compute sym. pct. change (spc) problem? > > >

1 0

Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer
by Knut J Bjuland 11 Aug '11

11 Aug '11

Hi Bruce I am now responding to the list as well. I have a group with different subjects where I wish to correlate thalamus volume with gender difference. Though I have extract the data using asegstats2table. I wish to be sure that the group difference is correct. Due to this reason I wish to use multiple comparsion within Freesurfer for instant FDR. I have some trouble figuring out --iv volmeasfile or how to use an label to include thalamus but exclude everything else? Knut J Knut J On 08/11/2011 08:42 PM, Bruce Fischl wrote: > Hi Knut > > you should respond onlist so Doug and Nick can answer! If all you want > is thalamic volume then why do you have multiple comparisons? You only > have one number/subject, no? > Bruce > > On Thu, 11 Aug 2011, Knut J Bjuland wrote: > >> Hi Bruce >> >> I wish to use a group difference analysis using gender and correlate >> thalamus volume with IQ, and then apply multiple comparisons using FDR >> or Monte Carlo simulation. Do you have any links to a good tutorial? I >> inted to use mris_preproc and mris_glm for voulmetirc analysis, but I >> have some trouble figuring out --iv volmeasfile? >> >> Cheers >> Knut J >> >> >> Knut J >> >> On 08/11/2011 08:03 PM, Bruce Fischl wrote: >>> Hi Knut >>> >>> you don't need to register it since the segmentation (aseg) is created >>> from the same data as the surface. What kind of analysis are you >>> thinking of doing? >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 11 Aug 2011, Knut J Bjuland wrote: >>> >>>> I am working to do a volumetric analysis in Freesurfer using >>>> Thalamus. I >>>> do not know if this is the correct way to go. Should I first register >>>> thalamus to a surface using tkregister? There was also another post on >>>> this list, which suggested using tkregister2? I am also search to >>>> find >>>> a tutorial on how to create a volmask and the use it to calculate >>>> statistic in Freesurfer for Thalamus. >>>> >>>> Knut J >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. >>> >>> >>> >> >> >> > >

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Freesurfer August 2011